This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
I added the option to provide a single coordinate file for the optimization steps instead of several coordinate files (one for each replica), useful for the case of water perturbations in which we skip steps a to c of the pipeline. The code in reeds/modules/_do_RE_EDS_Optimization.py automatically creates copies of the provided input coordinates to match the number of s replicas.
Description
I added the option to provide a single coordinate file for the optimization steps instead of several coordinate files (one for each replica), useful for the case of water perturbations in which we skip steps a to c of the pipeline. The code in
reeds/modules/_do_RE_EDS_Optimization.pyautomatically creates copies of the provided input coordinates to match the number of s replicas.Status